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(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI DUTPASE WITH DUPNP AND CA2+
 
Authors :  G. R. Hemsworth, D. Gonzalez-Pacanowska, K. S. Wilson
Date :  03 Feb 12  (Deposition) - 07 Aug 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  All Alpha Ntp Pyrophosphohydrolase, All Alpha Ntp Pyrophosphatase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. R. Hemsworth, D. Gonzalez-Pacanowska, K. S. Wilson
On The Catalytic Mechanism Of Dimeric Dutpases.
Biochem. J. V. 456 81 2013
PubMed-ID: 24001052  |  Reference-DOI: 10.1042/BJ20130796

(-) Compounds

Molecule 1 - DEOXYURIDINE TRIPHOSPHATASE
    Chains: A
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-YSBLLIC3C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TB927.7.5160
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691
    Strain: 427
    Synonym: DEOXYURIDINE TRIPHOSPHATE NUCLEOTIDOHYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2DUN1Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DUN2Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:48 , GLU A:51 , CA A:302 , DUN A:303 , HOH A:401 , HOH A:402BINDING SITE FOR RESIDUE CA A 301
2AC2SOFTWAREGLU A:48 , GLU A:51 , GLU A:76 , ASP A:79 , CA A:301 , DUN A:303 , HOH A:403BINDING SITE FOR RESIDUE CA A 302
3AC3SOFTWAREGLN A:21 , LEU A:24 , ASN A:25 , TRP A:41 , GLU A:48 , GLU A:51 , LYS A:59 , TRP A:60 , TRP A:61 , ASP A:79 , HIS A:82 , PHE A:83 , LYS A:208 , ASN A:212 , ARG A:215 , TYR A:220 , LYS A:227 , ASN A:235 , CA A:301 , CA A:302 , HOH A:403 , HOH A:404BINDING SITE FOR RESIDUE DUN A 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DKB)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:159 -Pro A:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DKB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DKB)

(-) Exons   (0, 0)

(no "Exon" information available for 4DKB)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:223
 aligned with Q57ZH3_TRYB2 | Q57ZH3 from UniProtKB/TrEMBL  Length:287

    Alignment length:279
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276         
         Q57ZH3_TRYB2     7 VSLSPLILRSLAELQDGLNTVVDKNWRQLRRPGDWSLAITMEAAELLDSYPWKWWKNVKAQPDLQNVKIELTDILHFSLSGAMQVSDENSGAVHKAEAGSNGESGKHWCYFDQPRALPAAGGAEYVACVETPGSSLSAPVSADECDLADFMFFPLSDTNNALASFQNIIRLASLQRFQLVTSAVIAAADDIGFNLVAYYVAKHTLNGIRQMKGYKDGTYVKVQKGVEDNELLHGCISPFSLDDVTNEGNYKTKWDDIMHRVYDAFGTPKEERLNIGHWL 285
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhh....--------------------------------------------------------hhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.........ee..ee...hhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhh..hhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dkb A   7 VSLSPLILRSLAELQDGLNTVVDKNWRQLRRPGDWSLAITMEAAELLDSYPWKWWKNVKAQPDLQNVKIELTDILHFSLSGAMQVSDEN--------------------------------------------------------DLADFMFFPLSDTNNALASFQNIIRLASLQRFQLVTSAVIAAADDIGFNLVAYYVAKHTLNGIRQMKGYKDGTYVKVQKGVEDNELLHGCISPFSLDDVTNEGNYKTKWDDIMHRVYDAFGTPKEERLNIGHWL 285
                                    16        26        36        46        56        66        76        86        |-         -         -         -         -         -     | 156       166       176       186       196       206       216       226       236       246       256       266       276         
                                                                                                                   95                                                      152
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4DKB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DKB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DKB)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q57ZH3_TRYB2 | Q57ZH3)
molecular function
    GO:0004170    dUTP diphosphatase activity    Catalysis of the reaction: dUTP + H2O = dUMP + diphosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q57ZH3_TRYB2 | Q57ZH3: 4dk2 4dk4 4dl8 4dlc

(-) Related Entries Specified in the PDB File

4dk2 4dk4 4dl8 4dlc